Played with a little in Alice when the girls get their first training bras and none of them are developed enough to show so Joanne stuffs her bra with tissues to make it appear that she's got huge breasts. Nobody's fooled for even a second.
In thisCaptain SNES: The Game Masta strip, Lucca is implied to suffer from this trope via an unexpected revelation from Gato, who thought he was praising her and the signs of her "perfection" but ended up giving a Compliment Backfire speech. The main problem is she made the mistake of giving him a rough neural map of her brain as part of his AI, which apparently included her memories as well.
Eerie Cuties: Brooke is pretty confident, so she doesn't usually concern herself about her looks, though there isa certain area she feels she's lacking in. But she got over it, once she started dating.
Sarah from El Goonish Shive doesn't normally seem bothered by her relative lack of endowment, but sometimes it becomes an issue....
In her sometimes semi-autobiographical webcomic The Fart Party the author/artist Julia Werz tells of the day in the 7th grade when a cute guy that she had a crush on sat next to her in the lunch room and out of the blue asked her what her bra size was. She was so surprised that she immediately blurted out "32AA" without thinking and was known as "Tiny Tits" for the rest of the school year. 
Karin-dou 4koma: Seren and Tamaryu are very sensitive about their flatness. Seren's reactions in particular range from fury, to padding her chest, to locking herself in her room. But somehow, her genuine angst is actually deliberate, to make her immortality more interesting. Her unsealed form is actually reasonably endowed.
MegaTokyo. Although she doesn't seem too self-conscious about it, it's been noted that Nanasawa Kimiko is rather flat-chested — both in her initial appearance at Anna Miller's, when she apparently was wearing inserts to work, and again during Piro's conversation with Tsubasa over the internet after Kimiko's radio outburst makes her an instant star.
Kiley from Ménage à 3, so much so that when she dreams of being a professional therapist, she also dreams of having large breasts to go along with it, and when Yuki mentioned that her girlfriend had small breasts too, she cried tears of joy. Her introductory strip even had her comparing herself unfavorably with Didi, who later became her girlfriend.
A minor source of angst for Wonderella in The Non-Adventures of Wonderella, to the point that in this comic she goes to Dr. Shark for breast augmentation. He asks her to not do it just out of societal pressure and consider what body feels right for her. She opts to keep her breasts the way they are...and get ass lasers and rocket feet instead.
Violet of The Noordegraaf Files is the flattest memeber of the main cast (she is mistaken for male by the protagonist), and while it isn't flat-out stated she's embarrassed about her lack of bustiness, it's heavily implied to be one of the reasons her jealousy of the heroine, Katrina, exists. However, it's revealed that she has a darker reason for her angst than just jealousy - sometime in her Dark and Troubled Past her breasts had been cut off. Despite all this, she has a boyfriend who loves her, and is the only girl in the main cast in a committed relationship.
In Peter Is the Wolf, we meet Cherry, a Chinese-American Were-Raccoon-Dog (don't you dare call her a Tanuki!) of modest proportions in human form who is inordinatly proud of the D-cups she sports in were-form... until she sees the were-forms of Sarah the Werewolf and Ashley the Were-Vixen. Sarah herself, in her human form, isn't exactly big either, thought it seems to vary from page to page.
In Rascals, Ravin, the female mouse character, is often frustrated with her competitions well endowedness as seen in the Hot Springs arc.
Though Giancarlo uses her small bust as an insult, Cecil seemed to be at least slightly interested. If only for verification.
Although we don't see her angsting over it much, Ellen "Elf" Foxworthy of Schlock Mercenary does get teased early on that when not in her much curvier powered armor, she "doesn't get mistaken for a woman" very much, and apparently joined up with the mercenaries under the pretense of being a boy. Later on when she gets a full body rebuild, her two main requests are longer legs and bigger boobs.
Quinn from Shotgun Shuffle has held a secret grudge with her roommate Ellie for years over this.
Flora from TwoKinds, mostly as compared to other Keidrans(Kat and Natani in particular). Her human lover Trace certainly doesn't seem to mind...
A huge part of the backstory of Tara, from Welcome to Chastity, who was a D-cup in a town where breasts as big as a girl's head are considered average. This made Tara a flat chested by town's standards which made her a target of bullying from the her bustier classmates and unattractive to most guys. Though it turns out she was just a late bloomer and eventually becomes one the bustiest women in town, which turns things around for her considerably. Though it's actually implied that she grew as much because Gwen, her sister Rayya's BF and the witch in who cursed the town grew Tara's chest because she wanted to spend time with Rayya herself without Tara butting in.